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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttggttataccctgctgctggatatctttttctgttggcaagcattagttggccattataatttttttagcaatgcatacttctatttgaaagtaaaaactgatttgtgttcataagttctaatctttcttttttcccccgttgttttccttggtgttaaatttcagGAGTTTGAGCCGTTAATACAGAAGCCTTTTTCTATTGTCTACTTCCACTCTGCTGCATCTTTGCAGGT

Basic information

species Glycine max
transcript GLYMA20G03330.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G03330.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv01s0011g00870.t01 (Vitis vinifera), 3'ss of exon 9
gtaatttggttataccctgctgctggatatctttttctgttggcaagcattagttggccattataatttttttagcaatgcatacttctatttgaaagtaaaaactgatttgtgttcataagttctaatctttcttttttcccccgttgttttccttggtgttaaatttcagGAGTTTGAGCCGTTAATACAGAAGCCTTTTTCTATTGTCTACTTCCACTCTGCTGCATCTTTGCAGGT
                                                                 | | |||  |       |  |  |||   |  | ||    |   |||  ||  | | || | ||    |  |  ||    |  || ||  |||   ||||||||||||||||||||||  | ||||||||||||| | ||||||| ||||||||||| || ||||| |||||| |
-----------------------------------------------------------------actctttctgatgcttgtgttcttat---actgcaatgtttttcttgaatttctca-ttgttatggagcactgatcattggaagtcttgattg---ttaaatttcagGAGTTTGAGCCTGTGATACAGAAGCCTTATACTATTGTTTACTTCCACTCAGCAGCATCGTTGCAGAT
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|209714625|gb|BW654138.1|BW654138
EST:     TTTTACTTAGGTGCCTTGATCTGGAGCGATTTGTGCTCTATGTGGTGAAG                         GAGTTTGAGCCGTTAATACAGAAGCCTTTTTCTATTGTCTACTTCCACTCT
genomic: TTTTACTTAGGTGCCTTGATCTGGAGCGATTTGTGCTCTATGTGGTGAAGgtaatttggt ... taaatttcagGAGTTTGAGCCGTTAATACAGAAGCCTTTTTCTATTGTCTACTTCCACTCT
EST: gi|298172645|gb|HO019685.1|HO019685
EST:     TTTTACTTAGGTGCCTTGATCTGGAGCGATTTGTGCTCTATGTGGTGAAG                         GAGTTTGAGCCGTTAATACAGAAGCCTTTTTCTATTGTCTACTTCCACTCC
genomic: TTTTACTTAGGTGCCTTGATCTGGAGCGATTTGTGCTCTATGTGGTGAAGgtaatttggt ... taaatttcagGAGTTTGAGCCGTTAATACAGAAGCCTTTTTCTATTGTCTACTTCCACTCT
EST: gi|6482215|gb|AW201486.1|AW201486
EST:     TTTTACTTAGGTGCCTTGATCTGGAGCGATTTGTGCTCTATGTGGTGAAG                         GAGTTTGAGCCGTTAATACAGAAGCCTTTTTCTATTGTCTACTTCCACTCT
genomic: TTTTACTTAGGTGCCTTGATCTGGAGCGATTTGTGCTCTATGTGGTGAAGgtaatttggt ... taaatttcagGAGTTTGAGCCGTTAATACAGAAGCCTTTTTCTATTGTCTACTTCCACTCT
EST: gi|21887828|gb|BQ741041.1|BQ741041
EST:     TTTTACTTAGGTGCCTTGATCTGGAGCGATTTGTGCTCTATGTGGTGAAG                         GAGTTTGAGCCGTTAATACAGAAGCCTTTTTCTATTGTCTACTTCCACTCT
genomic: TTTTACTTAGGTGCCTTGATCTGGAGCGATTTGTGCTCTATGTGGTGAAGgtaatttggt ... taaatttcagGAGTTTGAGCCGTTAATACAGAAGCCTTTTTCTATTGTCTACTTCCACTCT
EST: gi|22524022|gb|BU082833.1|BU082833
EST:     TTTTACTTAGGTGCCTTGATCTGGAGCGATTTGTGCTCTATGTGGTGAAG                         GAGTTTGAGCCGTTAATACAGAAGCCTTTTTCTATTGTCTACTTCCACTCT
genomic: TTTTACTTAGGTGCCTTGATCTGGAGCGATTTGTGCTCTATGTGGTGAAGgtaatttggt ... taaatttcagGAGTTTGAGCCGTTAATACAGAAGCCTTTTTCTATTGTCTACTTCCACTCT
EST: gi|193583007|gb|FK543219.1|FK543219
EST:     TTTTACTTAGGTGCCTTGATCTGGAGCGATTTGTGCTCTATGTGGTGAAG                         GAGTTTGAGCCGTTAATACAGAAGCCTTTTTCTATTGTCTACTTCCACTCT
genomic: TTTTACTTAGGTGCCTTGATCTGGAGCGATTTGTGCTCTATGTGGTGAAGgtaatttggt ... taaatttcagGAGTTTGAGCCGTTAATACAGAAGCCTTTTTCTATTGTCTACTTCCACTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataagttctaatctttcttttttcccccgttgttttccttggtgttaaatttcagGAGTTTGAGCCGTTAATACAGAAGCCTTTTTCTATTGTCTACTTCCACTCTGCTGCATCTTTGCAGGT
     ttctaat  putative branch site (score: 2)
           tctttcttttttcccc  CT-rich tract
        taatctttctttttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttggttataccctgctgctggatatctttttctgttggcaagcattagttggccattataatttttttagcaatgcatacttctatttgaaagtaaaaactgatttgtgttcataagttctaatctttcttttttcccccgttgttttccttggtgttaaatttcagGAGTTTGAGCCGTTAATACAGAAGCCTTTTTCTATTGTCTACTTCCACTCTGCTGCATCTTTGCAGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC